How to encrypt decrypt with RSA keys in java

I think you're having problems reading PEM files. The JPA doesn't directly support the PEM format. You have two options, either convert them to DER encoded files (you can use openSSL to do this) or the you can use the bouncy castle API to read (or write) PEM files. the class you'd be interested in is called PEMReader (and maybe also PEMWriter). Here is the Javadoc on the bouncycastle website.

Solution:

Thanks to @Sanjeev, using the bouncy castle API, I was able to encrypt/decrypt with the keys generated by openssl

public static void main(String[] args) throws IOException {

    Security.addProvider(new BouncyCastleProvider());

    KeyPair keyPair = readKeyPair(new File(PRIVATE_PATH), "pass"); 
    // if the private key is not encripted, pass can be anything.
    Key publickey = readPublicKey(new File(PUBLIC_PATH), "pass"); 
    Base64 base64 = new Base64();
    String text = "this is the input text";
    byte[] encripted;
    System.out.println("input:\n" + text);
    encripted = encrypt(keyPair.getPublic(), text);
    System.out.println("cipher:\n" + base64.encodeAsString(encripted));
    System.out.println("decrypt:\n" + decrypt(keyPair.getPrivate(), encripted));        
}

private static byte[] encrypt(Key pubkey, String text) {
    try {
        Cipher rsa;
        rsa = Cipher.getInstance("RSA");
        rsa.init(Cipher.ENCRYPT_MODE, pubkey);
        return rsa.doFinal(text.getBytes());
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}


private static String decrypt(Key decryptionKey, byte[] buffer) {
    try {
        Cipher rsa;
        rsa = Cipher.getInstance("RSA");
        rsa.init(Cipher.DECRYPT_MODE, decryptionKey);
        byte[] utf8 = rsa.doFinal(buffer);
        return new String(utf8, "UTF8");
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}

private static KeyPair readKeyPair(File privateKey, String keyPassword) throws IOException {
    FileReader fileReader = new FileReader(privateKey);
    PEMReader r = new PEMReader(fileReader, new DefaultPasswordFinder(keyPassword.toCharArray()));
    try {
        return (KeyPair) r.readObject();
    } catch (IOException ex) {
        throw ex;
    } finally {
        r.close();
        fileReader.close();
    }
}

private static Key readPublicKey(File privateKey, String keyPassword) throws IOException {
    FileReader fileReader = new FileReader(privateKey);
    PEMReader r = new PEMReader(fileReader, new DefaultPasswordFinder(keyPassword.toCharArray()));
    try {
        return (RSAPublicKey) r.readObject();
    } catch (IOException ex) {
        throw ex;
    } finally {
        r.close();
        fileReader.close();
    }
}